Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs

Jun Ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants were conserved in the mouse genome. Of the 20 392 total human AS variants, however, 59% consisted of all conserved exons. Comparing AS patterns between human and mouse transcripts revealed that only 431 transcripts from 189 loci were perfectly conserved AS variants. To exclude the possibility that the full-length human cDNAs used in the present study, especially those with retained introns, were cloning artefacts or prematurely spliced transcripts, we experimentally validated 34 such cases. Our results indicate that even retained-intron type transcripts are typically expressed in a highly controlled manner and interact with translating ribosomes. We found non-conserved AS exons to be predominantly outside the coding sequences (CDSs). This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes.

Original languageEnglish
Pages (from-to)6386-6395
Number of pages10
JournalNucleic acids research
Volume36
Issue number20
DOIs
Publication statusPublished - 2008 Nov 28
Externally publishedYes

Fingerprint

Alternative Splicing
Genomics
Complementary DNA
Exons
Introns
Species Specificity
Human Genome
Ribosomes
Artifacts
Organism Cloning
Genome
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Low conservation and species-specific evolution of alternative splicing in humans and mice : Comparative genomics analysis using well-annotated full-length cDNAs. / Takeda, Jun Ichi; Suzuki, Yutaka; Sakate, Ryuichi; Sato, Yoshiharu; Seki, Masahide; Irie, Takuma; Takeuchi, Nono; Ueda, Takuya; Nakao, Mitsuteru; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi.

In: Nucleic acids research, Vol. 36, No. 20, 28.11.2008, p. 6386-6395.

Research output: Contribution to journalArticle

Takeda, JI, Suzuki, Y, Sakate, R, Sato, Y, Seki, M, Irie, T, Takeuchi, N, Ueda, T, Nakao, M, Sugano, S, Gojobori, T & Imanishi, T 2008, 'Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs', Nucleic acids research, vol. 36, no. 20, pp. 6386-6395. https://doi.org/10.1093/nar/gkn677
Takeda, Jun Ichi ; Suzuki, Yutaka ; Sakate, Ryuichi ; Sato, Yoshiharu ; Seki, Masahide ; Irie, Takuma ; Takeuchi, Nono ; Ueda, Takuya ; Nakao, Mitsuteru ; Sugano, Sumio ; Gojobori, Takashi ; Imanishi, Tadashi. / Low conservation and species-specific evolution of alternative splicing in humans and mice : Comparative genomics analysis using well-annotated full-length cDNAs. In: Nucleic acids research. 2008 ; Vol. 36, No. 20. pp. 6386-6395.
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